Being lack of specific immune system, both enzymes and non-enzymatic antioxidants play crucial roles in immune of invertebrates. In the present study, in order to investigate immune roles of enzyme (thioredoxin, TRX) and antioxidants (carotenoids), Golden scallops with golden shell and golden muscle rich in carotenoids content and Brown scallops with brown shell and white muscle less carotenoids content of the noble scallop Chlamys nobilis were challenged by Vibrio parahaemolyticus for 48 h. Firstly, a cDNA of TRX protein gene from the scallop (named as CnTRX) was cloned and characterized. The cDNA contains 1280 bp, consisting of a 5′ -UTR of 99 bp, a long 3′ -UTR of 860 bp and a 321 bp open reading frame (ORF) encoding 106 amino acids. Phylogenetic analysis showed that CnTRX had a closer evolution relationship with TRX from Chlamys farreri. CnTRX was ubiquitously expressed in all examined tissues including intestine, adductor, mantle, gonad, gill, kidney, hepatopancreas and hemolymph, and the highest expression level was detected in the hemolymph. Next, CnTRX transcripts were significantly up-regulated in V. parahaemolyticus group in comparison with PBS control group. Moreover, CnTRX transcripts were significantly higher in Golden scallops than that of Brown ones at 6 h, 12 h and 24 h with bacteria challenge (P < 0.05). The present result indicates that both CnTRX and carotenoids are important factors involved in the immune defense against bacteria challenge in the noble scallop.